/* Score.c -- Matt scoring function.
 *
 * Author: Matt Menke (2007)
 *
 * Matt is licensed under the GNU public license version 2.0. 
 *
 * If you would like to license Matt in an enviroment where the GNU public license is 
 * unacceptable (such as inclusion in a non-GPL software package) comercial Matt
 * licensing is available through the MIT and Tufts offices of Technology Transfer. 
 * Contact betawrap@csail.mit.edu or cowen@cs.tufts.edu for more information.
 */


/* Negative log p-value table, indexed by 1000*RMSD.  First 31 values come from a log-log regression.
 * Might reduce them to more reasonable values at some point, though an RMSD of 0.03 Angstroms on random
 * structures is very unlikely, unless one protein was used to model another.
 */
#include "Score.h"

const double RMSDTable[3001] = {
	 22.48300000000000,
	 22.48300000000000,
	 14.25664538781148,
	 10.92169821004553,
	  9.04024986495603,
	  7.80712573188103,
	  6.92553388841856,
	  6.25829208565556,
	  5.73249284089706,
	  5.30549712188372,
	  4.95055922508055,
	  4.64997895971138,
	  4.39153497168770,
	  4.16649331491869,
	  3.96843174836714,
	  3.79251306015591,
	  3.63501835257027,
	  3.49303734924338,
	  3.36425704188723,
	  3.24681388031330,
	  3.13918815742260,
	  3.04012709468694,
	  2.94858787036382,
	  2.86369477192437,
	  2.78470652490879,
	  2.71099106851394,
	  2.64200585782515,
	  2.57728232084149,
	  2.51641347605760,
	  2.45904398053706,
	  2.30258509299405,
	  2.26612078163525,
	  2.26612078163525,
	  2.22149207137241,
	  2.20858436714490,
	  2.13600326840702,
	  2.09666120955781,
	  2.05203249929497,
	  2.02532622077007,
	  2.00176961363879,
	  1.98069751050723,
	  1.94759462281171,
	  1.93447516631455,
	  1.90501022336318,
	  1.88669678465808,
	  1.85444315513885,
	  1.82853634470047,
	  1.79743936413239,
	  1.78204715590517,
	  1.76097505277360,
	  1.74070455392155,
	  1.71688038822194,
	  1.69559449565259,
	  1.67635771088201,
	  1.65406662269694,
	  1.63330726396061,
	  1.61514352915701,
	  1.59731298807081,
	  1.57932334073823,
	  1.55841259300065,
	  1.53772827477002,
	  1.52259500815527,
	  1.50368024760607,
	  1.48707760421290,
	  1.47332423276348,
	  1.45956785701040,
	  1.44697428413587,
	  1.43330520158790,
	  1.41978315688866,
	  1.40734513205582,
	  1.39286512609411,
	  1.38135115572981,
	  1.36952027123248,
	  1.35870682697842,
	  1.34642454206780,
	  1.33406288459342,
	  1.32271884808653,
	  1.31043618809749,
	  1.29794061107370,
	  1.28680173269151,
	  1.27672372823129,
	  1.26555535930557,
	  1.25657738783510,
	  1.24655441380997,
	  1.23604133434097,
	  1.22614532288830,
	  1.21627785092719,
	  1.20712508857875,
	  1.19877348634486,
	  1.18747104429219,
	  1.17706087025592,
	  1.16689215965966,
	  1.15891656779654,
	  1.15131010803897,
	  1.14434856000664,
	  1.13638462806066,
	  1.12810520500424,
	  1.12069695066817,
	  1.11350097127273,
	  1.10414223979434,
	  1.09582401547454,
	  1.08848374210446,
	  1.08158180863563,
	  1.07280598198268,
	  1.06550804504499,
	  1.05906437151365,
	  1.05208874282399,
	  1.04553450539574,
	  1.03817979395615,
	  1.03139828609152,
	  1.02487281188492,
	  1.01832569066116,
	  1.01182859963226,
	  1.00513963435466,
	  0.99922816958916,
	  0.99337153435007,
	  0.98623547455231,
	  0.97985456524856,
	  0.97432255108949,
	  0.96883781729212,
	  0.96315355362676,
	  0.95817950718338,
	  0.95238819238761,
	  0.94664617121112,
	  0.94141843514270,
	  0.93544067777758,
	  0.93032661207969,
	  0.92452431592037,
	  0.91948008974475,
	  0.91361341960732,
	  0.90909743676538,
	  0.90425774040148,
	  0.89935286242886,
	  0.89495122945323,
	  0.89078187842950,
	  0.88605858721667,
	  0.88165769557256,
	  0.87738371615086,
	  0.87280591159445,
	  0.86891534384541,
	  0.86476664021923,
	  0.86036232683026,
	  0.85590845022431,
	  0.85183440734269,
	  0.84759218466689,
	  0.84337024734298,
	  0.83988768935250,
	  0.83612433268073,
	  0.83240480218245,
	  0.82865234689134,
	  0.82491952107862,
	  0.82152243784460,
	  0.81729908945574,
	  0.81340814553895,
	  0.80966020474415,
	  0.80612752735288,
	  0.80232447413018,
	  0.79884193528322,
	  0.79548304483904,
	  0.79246335989652,
	  0.78932289003955,
	  0.78626155336800,
	  0.78334681703165,
	  0.78017705220354,
	  0.77698860020488,
	  0.77406108241526,
	  0.77101514499728,
	  0.76800559565140,
	  0.76496732874985,
	  0.76190230889501,
	  0.75916825022775,
	  0.75630423947280,
	  0.75336819911673,
	  0.75062813607359,
	  0.74805981445389,
	  0.74509209087539,
	  0.74248694274709,
	  0.73993146545716,
	  0.73744815948909,
	  0.73527163471205,
	  0.73302477315191,
	  0.73054036559907,
	  0.72790360491524,
	  0.72554181977683,
	  0.72308862720815,
	  0.72073861495064,
	  0.71815463740152,
	  0.71585439392176,
	  0.71355195380929,
	  0.71140889992545,
	  0.70919145862054,
	  0.70708751937413,
	  0.70490364453939,
	  0.70295161877706,
	  0.70101846103167,
	  0.69891927778415,
	  0.69686145767703,
	  0.69477297067469,
	  0.69275077366568,
	  0.69078043961884,
	  0.68871661963172,
	  0.68669246844989,
	  0.68466405974999,
	  0.68272890539278,
	  0.68081831315510,
	  0.67896156766810,
	  0.67698017873905,
	  0.67545711232317,
	  0.67344036688084,
	  0.67161608451775,
	  0.66977981849022,
	  0.66803362716694,
	  0.66625778588944,
	  0.66455304019209,
	  0.66291771713948,
	  0.66115380540451,
	  0.65952970120672,
	  0.65795624767679,
	  0.65626197904995,
	  0.65461361079033,
	  0.65302584187713,
	  0.65139343519818,
	  0.64976909229813,
	  0.64840330346197,
	  0.64667610221422,
	  0.64515994798820,
	  0.64363021751075,
	  0.64221129516321,
	  0.64072356449584,
	  0.63917839769557,
	  0.63769842404675,
	  0.63616192481235,
	  0.63470402462948,
	  0.63327090695522,
	  0.63194693115301,
	  0.63052868533015,
	  0.62914366085009,
	  0.62781893797267,
	  0.62650751821106,
	  0.62511352954691,
	  0.62381514795820,
	  0.62253413320438,
	  0.62124340134585,
	  0.61999645898556,
	  0.61865579049180,
	  0.61746427702558,
	  0.61630161011508,
	  0.61500705097851,
	  0.61384993018248,
	  0.61278509297408,
	  0.61166201030774,
	  0.61048169014951,
	  0.60941353481823,
	  0.60833848918607,
	  0.60732752097600,
	  0.60618900586195,
	  0.60504457562421,
	  0.60395991633759,
	  0.60275073763036,
	  0.60163385873153,
	  0.60051512720720,
	  0.59951479368667,
	  0.59833609862278,
	  0.59725938535350,
	  0.59612932722719,
	  0.59506831678125,
	  0.59398561677449,
	  0.59301345744864,
	  0.59202669926283,
	  0.59094877857534,
	  0.59006002443123,
	  0.58899262330048,
	  0.58803302502111,
	  0.58713827029377,
	  0.58626625237408,
	  0.58552128890128,
	  0.58455956937567,
	  0.58374313568109,
	  0.58287470183723,
	  0.58194761607743,
	  0.58108692711464,
	  0.58024084354214,
	  0.57937295841857,
	  0.57853407954913,
	  0.57763403662826,
	  0.57679882764310,
	  0.57596709202826,
	  0.57512815865923,
	  0.57428566462592,
	  0.57343615199397,
	  0.57253419828282,
	  0.57164675207367,
	  0.57086043162722,
	  0.57010486362003,
	  0.56927977851740,
	  0.56856790549017,
	  0.56778673479822,
	  0.56707333215590,
	  0.56635567482364,
	  0.56556955291156,
	  0.56481009037288,
	  0.56403672020949,
	  0.56325295714859,
	  0.56252886876643,
	  0.56183726375472,
	  0.56110835167627,
	  0.56034584239724,
	  0.55967486638678,
	  0.55900286129638,
	  0.55829070988160,
	  0.55765258464548,
	  0.55691930564882,
	  0.55626616465932,
	  0.55554437487031,
	  0.55480595200724,
	  0.55422356091396,
	  0.55355048718967,
	  0.55290506380605,
	  0.55226171658093,
	  0.55155420964454,
	  0.55088061756935,
	  0.55024060698382,
	  0.54956829539909,
	  0.54888890245906,
	  0.54824591996001,
	  0.54762354654492,
	  0.54706475329753,
	  0.54644603902079,
	  0.54579553215704,
	  0.54512881390065,
	  0.54449778796087,
	  0.54375045288709,
	  0.54308748390725,
	  0.54247490751647,
	  0.54188222534831,
	  0.54127032889333,
	  0.54071703682861,
	  0.54010273444311,
	  0.53956156673759,
	  0.53894191683303,
	  0.53835959734331,
	  0.53775542515172,
	  0.53712080245448,
	  0.53654960364800,
	  0.53595961548722,
	  0.53543534588735,
	  0.53488633789572,
	  0.53433015434444,
	  0.53384187355729,
	  0.53326268502443,
	  0.53278848214530,
	  0.53222950628320,
	  0.53168065224256,
	  0.53115607673371,
	  0.53069535843541,
	  0.53020169214700,
	  0.52966119334262,
	  0.52907424406773,
	  0.52855083089191,
	  0.52810448046207,
	  0.52757800223932,
	  0.52705569569504,
	  0.52649302122920,
	  0.52594302088259,
	  0.52541942773931,
	  0.52488064547510,
	  0.52445341562156,
	  0.52391997198367,
	  0.52342903285081,
	  0.52294749388305,
	  0.52248892207811,
	  0.52194980883746,
	  0.52145825129032,
	  0.52100849020560,
	  0.52054353716728,
	  0.52009043810084,
	  0.51956311664063,
	  0.51909078535996,
	  0.51866770879406,
	  0.51817613738900,
	  0.51769375670089,
	  0.51727362199697,
	  0.51681991152692,
	  0.51639367252623,
	  0.51589973750362,
	  0.51544123323819,
	  0.51500216089758,
	  0.51454832771600,
	  0.51412689744614,
	  0.51368808884394,
	  0.51332314902291,
	  0.51289129578922,
	  0.51239296312812,
	  0.51193466007224,
	  0.51147224406661,
	  0.51101346915475,
	  0.51055060717668,
	  0.51018365107638,
	  0.50978410171699,
	  0.50933428426564,
	  0.50889057066131,
	  0.50846817327278,
	  0.50804412959234,
	  0.50760579685422,
	  0.50716842269355,
	  0.50676728474048,
	  0.50632167924413,
	  0.50590466700975,
	  0.50557368640439,
	  0.50520323712886,
	  0.50481600081255,
	  0.50442453074285,
	  0.50407360761323,
	  0.50368358656016,
	  0.50324974422182,
	  0.50285143874336,
	  0.50246872493963,
	  0.50210643948539,
	  0.50171285962774,
	  0.50132741081055,
	  0.50093535952233,
	  0.50060760687771,
	  0.50021208445185,
	  0.49981247418245,
	  0.49947926440824,
	  0.49910536899004,
	  0.49872732911060,
	  0.49833308780651,
	  0.49794926844585,
	  0.49759266332758,
	  0.49718623488684,
	  0.49682379201940,
	  0.49641413499376,
	  0.49603397719754,
	  0.49569269036823,
	  0.49530914002883,
	  0.49493582592651,
	  0.49452527242524,
	  0.49417944828299,
	  0.49380587272632,
	  0.49345185691559,
	  0.49313613186062,
	  0.49268461662423,
	  0.49232554378035,
	  0.49196477388411,
	  0.49161399916689,
	  0.49130349266384,
	  0.49093291717545,
	  0.49056070285874,
	  0.49022166068756,
	  0.48985308244874,
	  0.48951986088350,
	  0.48916872827543,
	  0.48884355682580,
	  0.48848670782211,
	  0.48814886408065,
	  0.48784827259322,
	  0.48745886437051,
	  0.48717758806169,
	  0.48685335376570,
	  0.48649092539712,
	  0.48614733939054,
	  0.48578845637411,
	  0.48545740179924,
	  0.48511784698712,
	  0.48478338363234,
	  0.48448329501607,
	  0.48417915356550,
	  0.48385524499885,
	  0.48352512854104,
	  0.48318659569707,
	  0.48286428934682,
	  0.48256483122060,
	  0.48223014792016,
	  0.48189824939601,
	  0.48157801092789,
	  0.48125828440355,
	  0.48095457386773,
	  0.48061593773758,
	  0.48031099225931,
	  0.47992936116744,
	  0.47960785663347,
	  0.47931762549703,
	  0.47902123319509,
	  0.47866833125299,
	  0.47835759209096,
	  0.47804733497422,
	  0.47774409802594,
	  0.47742826091044,
	  0.47715204030333,
	  0.47683496600680,
	  0.47650972742689,
	  0.47620232148236,
	  0.47589970705260,
	  0.47560617654073,
	  0.47529800176840,
	  0.47498815103724,
	  0.47464658091356,
	  0.47432487882605,
	  0.47404434834197,
	  0.47372147620723,
	  0.47339912446458,
	  0.47311775851461,
	  0.47278361812988,
	  0.47247763547296,
	  0.47221028412079,
	  0.47190305951632,
	  0.47158150923657,
	  0.47129002249725,
	  0.47094627653152,
	  0.47066623374240,
	  0.47037607694378,
	  0.47008843852073,
	  0.46981378376152,
	  0.46953322888694,
	  0.46928231930692,
	  0.46900459513840,
	  0.46870225192134,
	  0.46837956207592,
	  0.46805946888959,
	  0.46773574012846,
	  0.46745187138561,
	  0.46714772972529,
	  0.46678419466078,
	  0.46645222042081,
	  0.46617016632056,
	  0.46589467285595,
	  0.46559699112536,
	  0.46528541349592,
	  0.46500704436633,
	  0.46473518994031,
	  0.46443922772863,
	  0.46414370283804,
	  0.46389335807251,
	  0.46363723184454,
	  0.46334288875998,
	  0.46303885108184,
	  0.46274538668258,
	  0.46248870561395,
	  0.46226059672275,
	  0.46194409789901,
	  0.46168039566312,
	  0.46143713187792,
	  0.46113396919119,
	  0.46084929446414,
	  0.46057702760061,
	  0.46029314394523,
	  0.46002163262383,
	  0.45974451243595,
	  0.45944987068091,
	  0.45914374411535,
	  0.45884006869193,
	  0.45853487337711,
	  0.45825387161914,
	  0.45792982491715,
	  0.45765755765864,
	  0.45737581613449,
	  0.45707087954648,
	  0.45675266775069,
	  0.45641928531335,
	  0.45606885281163,
	  0.45576980706349,
	  0.45546535735599,
	  0.45520031726887,
	  0.45493173807064,
	  0.45463827058364,
	  0.45438790057593,
	  0.45408748235675,
	  0.45380491989442,
	  0.45353048129080,
	  0.45326027618336,
	  0.45297695316224,
	  0.45269210766200,
	  0.45239422402176,
	  0.45209103084119,
	  0.45182659206430,
	  0.45155676525790,
	  0.45131786113038,
	  0.45101820129315,
	  0.45072851189621,
	  0.45047918158218,
	  0.45021876364118,
	  0.44993971369439,
	  0.44966484125352,
	  0.44932603616992,
	  0.44907089190795,
	  0.44881795908075,
	  0.44854085542889,
	  0.44831116943332,
	  0.44800094756253,
	  0.44775311605622,
	  0.44748310420219,
	  0.44721158510500,
	  0.44697033619199,
	  0.44669577891910,
	  0.44647565839023,
	  0.44618874637083,
	  0.44593757069628,
	  0.44565142900736,
	  0.44539165497421,
	  0.44512481037158,
	  0.44488791369005,
	  0.44466607760416,
	  0.44441311518705,
	  0.44412545943921,
	  0.44383821682637,
	  0.44354219967321,
	  0.44323561305066,
	  0.44296429979812,
	  0.44273177675993,
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};


double RMSDScoreSimple(double rmsd, int length) {
	if (rmsd > 2.8) return 0;
	else {
		/* linear interpolation of table values. */
		double rmsd1000 = 1000*rmsd;
		int i = (int)rmsd1000;
		double r = rmsd1000 - i;
		return length * (RMSDTable[i] * (1-r) + r * RMSDTable[i+1]);
	}
}

//*
double AngleScore(double angle) {
	if (angle<0.1) angle = 0.1;
	return -log((1 - cos(angle))/2);
}//*/

double AngleScoreHalfCos(double angleHalfCos) {
	/* cos(0.1/2).  The cutoff to avoid excessively large scores. */
	if (angleHalfCos < 0.99875026039496624) {
		return -log(1 - angleHalfCos*angleHalfCos);
	}
	/* Score for angle of 0.1. */
	return 5.9922979498967957;
}

double DisplacementScore(double displacement) {
	return (4-displacement);
}

